******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/470/470.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11338 1.0000 500 16607 1.0000 500 17193 1.0000 500 20952 1.0000 500 21342 1.0000 500 21415 1.0000 500 21433 1.0000 500 21601 1.0000 500 21732 1.0000 500 21797 1.0000 500 22017 1.0000 500 22288 1.0000 500 22668 1.0000 500 23027 1.0000 500 23660 1.0000 500 23776 1.0000 500 23899 1.0000 500 24375 1.0000 500 24719 1.0000 500 25137 1.0000 500 25292 1.0000 500 25335 1.0000 500 263557 1.0000 500 269820 1.0000 500 3763 1.0000 500 4411 1.0000 500 7725 1.0000 500 7791 1.0000 500 7903 1.0000 500 8280 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/470/470.seqs.fa -oc motifs/470 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 30 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.226 G 0.243 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.226 G 0.243 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 21 llr = 252 E-value = 4.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::8114:31:41:332:82:6 pos.-specific C 571491551a5576149:6a: probability G 12:::3:2:::2::3:1:::3 matrix T 4114:24:7:113133:22:1 bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * * Relative 1.3 * * * ** * Entropy 1.1 * * * ** * (17.3 bits) 0.9 * * * * ** * 0.6 *** * **** ** ***** 0.4 ***** ***** ** ***** 0.2 ************** ****** 0.0 --------------------- Multilevel CCATCACCTCCCCCTCCACCA consensus T C GTA A TAAT T G sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 16607 467 6.28e-10 CCTCCGTCCT CCTCCACCTCCCCATCCACCA CCTCAATGCA 25137 417 9.21e-10 AGAGGGTGAA CCATCTCATCACCATCCACCA TCACGCCCCC 8280 430 1.66e-08 CCAACACCAA CCACCACACCACCAAACACCA ACTCCAGAAT 4411 76 3.29e-08 GACAACACTA TCCTCGTGTCCGCCGCCACCA CTATTTGTCT 7903 33 1.45e-07 GGAGGTGGGC TGATCGCCTCCTTCACCATCA TCATCCACAT 269820 145 2.82e-07 TGAACTGCCT CCATCGTCGCCGTCGCCATCA GTTGTGGATG 23899 463 3.14e-07 GCTTGGCACG CCACCGTGCCGACCGCCACCA ACGCAAAGAG 21732 284 4.76e-07 AGAAGGGGGT GCAAAGTCTCACCCACCACCG GACCCCTTCA 21601 423 1.04e-06 CCTCTCGCGC TCATCGAGTCACCAATCAACG TGGCTCGGCT 23776 477 1.37e-06 GCCTCTTCTT TCTTCTTCTCACTCCACATCA ACC 263557 422 1.78e-06 ACACACGTAG TCATCACAACACTCGTGATCG TGATATCAAT 24719 61 1.78e-06 GGCCGAGATA CCAGCCCCTCCCTCGTGAACA ATGCTTCGTC 25335 439 1.95e-06 TGATCATCAA TTATCACATCCATCGTCAACG TTACATTCAA 3763 441 2.12e-06 TTGAAACCCT CCCCCATGTCCTCTTTCACCT CAACCGAACC 11338 331 2.73e-06 CCCTCCTCCA CTACCATCTCACCATTCTTCT CCCTGAGACC 24375 88 3.22e-06 CATATCCTTC GCAACAGATCAGCATCCACCG TGCCATCGTC 22288 432 3.49e-06 CAGCCCCCCT CCACCTTCACTGCCTCGTCCA TAGGCTTAGC 7725 456 6.01e-06 TCGTCTCGGA CGACCCCCCCCCCCAGCACGA CATTGAGCAC 23660 438 9.29e-06 AGCAAAGACG TGTTAACGACCCCCTTCTCCA AAAGTTTTAA 23027 478 1.49e-05 GCAAGACACT TGACCTCATCTACTAACTCCA CT 21797 286 2.18e-05 GTGTATTGTG CAAACATCTCCTCTCACAACG AAGAGAACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16607 6.3e-10 466_[+1]_13 25137 9.2e-10 416_[+1]_63 8280 1.7e-08 429_[+1]_50 4411 3.3e-08 75_[+1]_404 7903 1.4e-07 32_[+1]_447 269820 2.8e-07 144_[+1]_335 23899 3.1e-07 462_[+1]_17 21732 4.8e-07 283_[+1]_196 21601 1e-06 422_[+1]_57 23776 1.4e-06 476_[+1]_3 263557 1.8e-06 421_[+1]_58 24719 1.8e-06 60_[+1]_419 25335 1.9e-06 438_[+1]_41 3763 2.1e-06 440_[+1]_39 11338 2.7e-06 330_[+1]_149 24375 3.2e-06 87_[+1]_392 22288 3.5e-06 431_[+1]_48 7725 6e-06 455_[+1]_24 23660 9.3e-06 437_[+1]_42 23027 1.5e-05 477_[+1]_2 21797 2.2e-05 285_[+1]_194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=21 16607 ( 467) CCTCCACCTCCCCATCCACCA 1 25137 ( 417) CCATCTCATCACCATCCACCA 1 8280 ( 430) CCACCACACCACCAAACACCA 1 4411 ( 76) TCCTCGTGTCCGCCGCCACCA 1 7903 ( 33) TGATCGCCTCCTTCACCATCA 1 269820 ( 145) CCATCGTCGCCGTCGCCATCA 1 23899 ( 463) CCACCGTGCCGACCGCCACCA 1 21732 ( 284) GCAAAGTCTCACCCACCACCG 1 21601 ( 423) TCATCGAGTCACCAATCAACG 1 23776 ( 477) TCTTCTTCTCACTCCACATCA 1 263557 ( 422) TCATCACAACACTCGTGATCG 1 24719 ( 61) CCAGCCCCTCCCTCGTGAACA 1 25335 ( 439) TTATCACATCCATCGTCAACG 1 3763 ( 441) CCCCCATGTCCTCTTTCACCT 1 11338 ( 331) CTACCATCTCACCATTCTTCT 1 24375 ( 88) GCAACAGATCAGCATCCACCG 1 22288 ( 432) CCACCTTCACTGCCTCGTCCA 1 7725 ( 456) CGACCCCCCCCCCCAGCACGA 1 23660 ( 438) TGTTAACGACCCCCTTCTCCA 1 23027 ( 478) TGACCTCATCTACTAACTCCA 1 21797 ( 286) CAAACATCTCCTCTCACAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 10.9255 E= 4.8e-006 -1104 121 -135 50 -245 156 -35 -150 154 -125 -1104 -91 -87 75 -235 67 -146 200 -1104 -1104 71 -125 23 -50 -245 107 -235 67 13 107 -3 -1104 -87 -66 -235 131 -1104 214 -1104 -1104 54 107 -235 -150 -87 121 -35 -91 -1104 166 -1104 9 13 134 -1104 -91 13 -125 23 31 -46 92 -235 31 -1104 192 -77 -1104 163 -1104 -1104 -50 -46 134 -1104 -18 -1104 207 -235 -1104 124 -1104 23 -150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 4.8e-006 0.000000 0.523810 0.095238 0.380952 0.047619 0.666667 0.190476 0.095238 0.761905 0.095238 0.000000 0.142857 0.142857 0.380952 0.047619 0.428571 0.095238 0.904762 0.000000 0.000000 0.428571 0.095238 0.285714 0.190476 0.047619 0.476190 0.047619 0.428571 0.285714 0.476190 0.238095 0.000000 0.142857 0.142857 0.047619 0.666667 0.000000 1.000000 0.000000 0.000000 0.380952 0.476190 0.047619 0.095238 0.142857 0.523810 0.190476 0.142857 0.000000 0.714286 0.000000 0.285714 0.285714 0.571429 0.000000 0.142857 0.285714 0.095238 0.285714 0.333333 0.190476 0.428571 0.047619 0.333333 0.000000 0.857143 0.142857 0.000000 0.809524 0.000000 0.000000 0.190476 0.190476 0.571429 0.000000 0.238095 0.000000 0.952381 0.047619 0.000000 0.619048 0.000000 0.285714 0.095238 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]CA[TC]C[AG][CT][CAG]TC[CA]C[CT][CA][TAG][CT]CA[CT]C[AG] -------------------------------------------------------------------------------- Time 8.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 21 llr = 242 E-value = 2.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :21:2426:165:72:3::4 pos.-specific C :31:11::2:1::11::1:: probability G a1:83:8:48218:3a4:a6 matrix T :47234:33:13123:29:: bits 2.1 * 1.9 * 1.7 * * * 1.5 * * * Relative 1.3 * * * ** Entropy 1.1 * * * * * * *** (16.6 bits) 0.9 * * ** * * * *** 0.6 * ** ** * ** * *** 0.4 * ** ** ***** * *** 0.2 **** ********* ***** 0.0 -------------------- Multilevel GTTGGAGAGGAAGAGGGTGG consensus C TTT TT GT TT A A sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 3763 233 1.06e-08 ATGGAGCTGC GTTGAAGAGGAAGAGGCTGG AGGCTTGGAG 23660 281 1.46e-08 GTGAGACCCA GTTGTAGAGGAGGATGTTGA AGTGAATGAT 8280 90 1.50e-07 CCGAGACTGA GATGGAGTGGTTGATGGTGA ACTCTGGCCA 24719 229 3.37e-07 TTGCAACGTC GCCGTCGACGATGATGATGA CACTGCAGGT 7791 151 5.75e-07 GGCAGGAACG GATGATGATAATGAAGATGA GTCAGGAGAA 25292 11 6.37e-07 GGTTTGACGT GTTGTTAACGTTGACGATGG CATTGCTGTT 23776 262 6.37e-07 CTATTGCCAG GCTGAAGACGAATAGGGCGA CGGATTCAAA 22017 271 9.51e-07 GTCAACTTGT GGAGAAGATGAAGCTGATGG GCCATCATAT 17193 190 9.51e-07 TGAAGCCGTT GCTGGATTCGAAGACGATGA CAACCAATTT 23899 191 1.15e-06 GAATCTGCTA GTTGTTGAAGAAGAAGGTTG AGGTTGCGTA 4411 270 2.01e-06 TATGCAGGCA GTGGATGTGGCAGTGGGTGG GCGGTGGAAT 21797 250 2.01e-06 GGATGCTGTG GTCTGTGATGATGCGGTTGG ATCTCTGTGT 22668 22 2.39e-06 ATCCCTTTCA TTTTCAGTTGAAGATGATGG ATTTATCCAA 21415 102 2.39e-06 TAAAATATTG GCTTTCGATGGAGTTGACGG TTGGCTTCGG 21342 23 2.39e-06 GTGAAGATCG GAATGAGAGAATGAGGTTGG TTAGAAAGGG 269820 382 4.32e-06 ACCGTTTGAC GCTTGAGTGAAACAAGGTGG CGAAGCCAGT 20952 201 7.46e-06 ACGAGAAAAT GATGCCAATGGAGTAGTTGG GAAAGATTAA 25137 396 8.04e-06 AATACCAAAG GCAGGTAGGGCAGAGGGTGA ACCATCTCAT 7903 143 8.65e-06 TGGATTCGGC GTTGTTGTCGGTATTGGCGG TGCTGGGAGG 22288 214 8.65e-06 GGAGGAGGTG GTTGTGGTGGGGTTGGGTGG GCTCTTCTAG 23027 409 2.12e-05 AATGGGATGT GGTGGTAATCGGGACGGTGA CTTGCTACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3763 1.1e-08 232_[+2]_248 23660 1.5e-08 280_[+2]_200 8280 1.5e-07 89_[+2]_391 24719 3.4e-07 228_[+2]_252 7791 5.7e-07 150_[+2]_330 25292 6.4e-07 10_[+2]_470 23776 6.4e-07 261_[+2]_219 22017 9.5e-07 270_[+2]_210 17193 9.5e-07 189_[+2]_291 23899 1.2e-06 190_[+2]_290 4411 2e-06 269_[+2]_211 21797 2e-06 249_[+2]_231 22668 2.4e-06 21_[+2]_459 21415 2.4e-06 101_[+2]_379 21342 2.4e-06 22_[+2]_458 269820 4.3e-06 381_[+2]_99 20952 7.5e-06 200_[+2]_280 25137 8e-06 395_[+2]_85 7903 8.7e-06 142_[+2]_338 22288 8.7e-06 213_[+2]_267 23027 2.1e-05 408_[+2]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=21 3763 ( 233) GTTGAAGAGGAAGAGGCTGG 1 23660 ( 281) GTTGTAGAGGAGGATGTTGA 1 8280 ( 90) GATGGAGTGGTTGATGGTGA 1 24719 ( 229) GCCGTCGACGATGATGATGA 1 7791 ( 151) GATGATGATAATGAAGATGA 1 25292 ( 11) GTTGTTAACGTTGACGATGG 1 23776 ( 262) GCTGAAGACGAATAGGGCGA 1 22017 ( 271) GGAGAAGATGAAGCTGATGG 1 17193 ( 190) GCTGGATTCGAAGACGATGA 1 23899 ( 191) GTTGTTGAAGAAGAAGGTTG 1 4411 ( 270) GTGGATGTGGCAGTGGGTGG 1 21797 ( 250) GTCTGTGATGATGCGGTTGG 1 22668 ( 22) TTTTCAGTTGAAGATGATGG 1 21415 ( 102) GCTTTCGATGGAGTTGACGG 1 21342 ( 23) GAATGAGAGAATGAGGTTGG 1 269820 ( 382) GCTTGAGTGAAACAAGGTGG 1 20952 ( 201) GATGCCAATGGAGTAGTTGG 1 25137 ( 396) GCAGGTAGGGCAGAGGGTGA 1 7903 ( 143) GTTGTTGTCGGTATTGGCGG 1 22288 ( 214) GTTGTGGTGGGGTTGGGTGG 1 23027 ( 409) GGTGGTAATCGGGACGGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14430 bayes= 9.72762 E= 2.1e-004 -1104 -1104 197 -250 -46 34 -135 67 -87 -125 -235 141 -1104 -1104 165 -18 -14 -125 45 31 71 -66 -235 50 -46 -1104 165 -250 124 -1104 -235 31 -245 7 65 31 -87 -224 173 -1104 113 -125 -3 -150 100 -1104 -77 31 -245 -224 173 -150 135 -125 -1104 -18 -46 -66 45 31 -1104 -1104 204 -1104 35 -224 82 -50 -1104 -66 -1104 167 -1104 -1104 197 -250 54 -1104 135 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 21 E= 2.1e-004 0.000000 0.000000 0.952381 0.047619 0.190476 0.285714 0.095238 0.428571 0.142857 0.095238 0.047619 0.714286 0.000000 0.000000 0.761905 0.238095 0.238095 0.095238 0.333333 0.333333 0.428571 0.142857 0.047619 0.380952 0.190476 0.000000 0.761905 0.047619 0.619048 0.000000 0.047619 0.333333 0.047619 0.238095 0.380952 0.333333 0.142857 0.047619 0.809524 0.000000 0.571429 0.095238 0.238095 0.095238 0.523810 0.000000 0.142857 0.333333 0.047619 0.047619 0.809524 0.095238 0.666667 0.095238 0.000000 0.238095 0.190476 0.142857 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.333333 0.047619 0.428571 0.190476 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.952381 0.047619 0.380952 0.000000 0.619048 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TC]T[GT][GTA][AT]G[AT][GTC]G[AG][AT]G[AT][GT]G[GA]TG[GA] -------------------------------------------------------------------------------- Time 16.35 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 16 llr = 187 E-value = 8.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 8:339713196:a267 pos.-specific C 17181:64914a:541 probability G ::3:::131::::3:2 matrix T 234:1321:::::1:: bits 2.1 * 1.9 ** 1.7 * ** 1.5 ** ** Relative 1.3 ** ** ** Entropy 1.1 * *** ***** * (16.9 bits) 0.9 ** *** ***** ** 0.6 ** *** ***** ** 0.4 ** **** ******** 0.2 **************** 0.0 ---------------- Multilevel ACTCAACCCAACACAA consensus TAA T A C GC sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 24375 120 3.97e-09 GCCATCGTCG ACGCAACACAACACAA CACAGTGAAA 25335 464 6.41e-08 TCAACGTTAC ATTCAACACAACAGCA GATTCAATCG 25292 471 4.97e-07 GCAGTCAGTC ATTCAATCCAACACAG CCACCTCCCT 25137 480 4.97e-07 ACGTGAGAAC ATACAAGACACCACAA ACAAC 24719 11 9.19e-07 GATACCACAG CCTCAACGCACCACAG CCCTTCAATC 8280 413 1.24e-06 CGTAAACAAC ACAAATACCAACACCA ACCACCACAC 263557 471 1.24e-06 TTCTCCTTCT TCTCAAACCAACAACA ACATCTCAAC 4411 484 1.36e-06 GCTCACACAA ATCAAACGCAACACAA C 21732 479 1.64e-06 CCGTACACGT ACACATCTCACCAACA ACCAAG 3763 472 2.13e-06 CAACCGAACC ATTCAACCCACCATCC GCATACCGAA 7903 478 2.31e-06 CCCCCTGACA ACGCAAGCAACCACAA CGACACC 22017 203 2.31e-06 TACTGAGTGA ACGAATTGCAACAGAA CGGTAAAGAG 20952 433 4.07e-06 TCGTGCAAGT TCGCAACACCCCAGAA ATGACAACGT 22668 453 5.50e-06 ATACTCTAAT TCTCCTCCCAACACAG ATTCGCCGAC 11338 293 6.80e-06 CGAATTATTC ACTCTTCACACCAGCC CACAGCCCAC 17193 456 1.74e-05 AGTTTTGGTC ACAAAATGGAACAACA TTTACTTTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24375 4e-09 119_[+3]_365 25335 6.4e-08 463_[+3]_21 25292 5e-07 470_[+3]_14 25137 5e-07 479_[+3]_5 24719 9.2e-07 10_[+3]_474 8280 1.2e-06 412_[+3]_72 263557 1.2e-06 470_[+3]_14 4411 1.4e-06 483_[+3]_1 21732 1.6e-06 478_[+3]_6 3763 2.1e-06 471_[+3]_13 7903 2.3e-06 477_[+3]_7 22017 2.3e-06 202_[+3]_282 20952 4.1e-06 432_[+3]_52 22668 5.5e-06 452_[+3]_32 11338 6.8e-06 292_[+3]_192 17193 1.7e-05 455_[+3]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=16 24375 ( 120) ACGCAACACAACACAA 1 25335 ( 464) ATTCAACACAACAGCA 1 25292 ( 471) ATTCAATCCAACACAG 1 25137 ( 480) ATACAAGACACCACAA 1 24719 ( 11) CCTCAACGCACCACAG 1 8280 ( 413) ACAAATACCAACACCA 1 263557 ( 471) TCTCAAACCAACAACA 1 4411 ( 484) ATCAAACGCAACACAA 1 21732 ( 479) ACACATCTCACCAACA 1 3763 ( 472) ATTCAACCCACCATCC 1 7903 ( 478) ACGCAAGCAACCACAA 1 22017 ( 203) ACGAATTGCAACAGAA 1 20952 ( 433) TCGCAACACCCCAGAA 1 22668 ( 453) TCTCCTCCCAACACAG 1 11338 ( 293) ACTCTTCACACCAGCC 1 17193 ( 456) ACAAAATGGAACAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14550 bayes= 10.5647 E= 8.6e-002 152 -185 -1064 -52 -1064 160 -1064 22 -6 -185 4 70 -6 173 -1064 -1064 174 -185 -1064 -210 139 -1064 -1064 22 -106 131 -96 -52 26 73 4 -210 -206 195 -196 -1064 184 -185 -1064 -1064 110 95 -1064 -1064 -1064 214 -1064 -1064 193 -1064 -1064 -1064 -48 114 4 -210 110 95 -1064 -1064 139 -85 -38 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 8.6e-002 0.750000 0.062500 0.000000 0.187500 0.000000 0.687500 0.000000 0.312500 0.250000 0.062500 0.250000 0.437500 0.250000 0.750000 0.000000 0.000000 0.875000 0.062500 0.000000 0.062500 0.687500 0.000000 0.000000 0.312500 0.125000 0.562500 0.125000 0.187500 0.312500 0.375000 0.250000 0.062500 0.062500 0.875000 0.062500 0.000000 0.937500 0.062500 0.000000 0.000000 0.562500 0.437500 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.187500 0.500000 0.250000 0.062500 0.562500 0.437500 0.000000 0.000000 0.687500 0.125000 0.187500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[CT][TAG][CA]A[AT]C[CAG]CA[AC]CA[CG][AC]A -------------------------------------------------------------------------------- Time 23.96 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11338 2.19e-04 292_[+3(6.80e-06)]_22_\ [+1(2.73e-06)]_149 16607 7.51e-06 466_[+1(6.28e-10)]_13 17193 3.40e-04 147_[+2(5.79e-05)]_22_\ [+2(9.51e-07)]_246_[+3(1.74e-05)]_29 20952 3.18e-04 200_[+2(7.46e-06)]_212_\ [+3(4.07e-06)]_52 21342 8.17e-03 22_[+2(2.39e-06)]_458 21415 1.96e-02 101_[+2(2.39e-06)]_379 21433 8.71e-01 500 21601 4.19e-03 422_[+1(1.04e-06)]_57 21732 2.17e-05 283_[+1(4.76e-07)]_174_\ [+3(1.64e-06)]_6 21797 2.32e-04 249_[+2(2.01e-06)]_16_\ [+1(2.18e-05)]_194 22017 6.04e-05 202_[+3(2.31e-06)]_52_\ [+2(9.51e-07)]_210 22288 3.22e-04 213_[+2(8.65e-06)]_198_\ [+1(3.49e-06)]_48 22668 9.90e-05 21_[+2(2.39e-06)]_411_\ [+3(5.50e-06)]_32 23027 1.69e-03 408_[+2(2.12e-05)]_49_\ [+1(1.49e-05)]_2 23660 3.09e-06 280_[+2(1.46e-08)]_137_\ [+1(9.29e-06)]_42 23776 1.35e-05 152_[+1(3.68e-05)]_88_\ [+2(6.37e-07)]_195_[+1(1.37e-06)]_3 23899 5.08e-06 190_[+2(1.15e-06)]_252_\ [+1(3.14e-07)]_17 24375 6.34e-07 87_[+1(3.22e-06)]_11_[+3(3.97e-09)]_\ 365 24719 1.86e-08 10_[+3(9.19e-07)]_34_[+1(1.78e-06)]_\ 147_[+2(3.37e-07)]_252 25137 1.79e-10 395_[+2(8.04e-06)]_1_[+1(9.21e-10)]_\ 42_[+3(4.97e-07)]_5 25292 5.29e-06 10_[+2(6.37e-07)]_440_\ [+3(4.97e-07)]_14 25335 4.07e-06 438_[+1(1.95e-06)]_4_[+3(6.41e-08)]_\ 21 263557 5.93e-05 320_[+3(2.53e-05)]_85_\ [+1(1.78e-06)]_28_[+3(1.24e-06)]_14 269820 1.19e-05 3_[+1(9.96e-06)]_120_[+1(2.82e-07)]_\ 216_[+2(4.32e-06)]_99 3763 1.94e-09 232_[+2(1.06e-08)]_188_\ [+1(2.12e-06)]_10_[+3(2.13e-06)]_13 4411 3.50e-09 75_[+1(3.29e-08)]_173_\ [+2(2.01e-06)]_194_[+3(1.36e-06)]_1 7725 9.56e-03 455_[+1(6.01e-06)]_24 7791 5.35e-03 105_[+2(6.40e-06)]_25_\ [+2(5.75e-07)]_330 7903 8.46e-08 32_[+1(1.45e-07)]_89_[+2(8.65e-06)]_\ 315_[+3(2.31e-06)]_7 8280 1.53e-10 89_[+2(1.50e-07)]_55_[+2(7.46e-06)]_\ 72_[+2(1.16e-05)]_136_[+3(1.24e-06)]_1_[+1(1.66e-08)]_19_[+1(2.32e-05)]_10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************